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Molecular mechanism of plasmid elimination by the DdmDE defense system
Open accessPreprint — published as 10.1126/science.adq0534
Abstract
Seventh pandemic Vibrio cholerae strains contain two hallmark pathogenicity islands that encode the DNA defense modules DdmABC and DdmDE. Here we use cryo-EM to reveal the mechanistic basis for plasmid defense by DdmDE. A cryo-EM structure of the DdmD helicase-nuclease reveals that it adopts an auto-inhibited dimeric architecture. The prokaryotic Argonaute protein DdmE uses a DNA guide to target plasmid DNA. A structure of the DdmDE complex, validated by in vivo mutational studies, shows that DNA binding by DdmE triggers disassembly of the DdmD dimer and loading of monomeric DdmD onto the non-target DNA strand. Finally, in vitro studies reveal that DdmD translocates in the 5’ to 3’ direction, while partially degrading the plasmid DNA. These findings provide critical insights into the architecture and mechanism of DdmDE systems in plasmid elimination.
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Metadata
- Authors
- Loeff, L., Adams, D. W., Chanez, C., Stutzmann, S., Righi, L., Blokesch, M., & Jinek, M.
- Affiliations
- University of Zurich (CH)
- École Polytechnique Fédérale de Lausanne (CH)
- Corresponding author
- Loeff, L.
- Venue
- Science
- Publisher
- openRxiv
- Published
- 2024-05-10
- Volume
- 385
- Issue
- 6705
- Pages
- 188-194
- ISSN
- 0036-8075 (ISSN-L)
- OpenAlex
- W4399619501
- Cited by
- 38
- References
- 1
- Citations by year
- 2026: 10 · 2025: 22 · 2024: 6
- FWCI
- 5.16
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nc-nd
- Locations
- Science (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Zurich Open Repository and Archive (University of Zurich) (acceptedVersion, cc-by-nc-nd)
- Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
- Zurich Open Repository and Archive (University of Zurich) (submittedVersion)
- Zurich Open Repository and Archive (University of Zurich)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Keywords
- plasmid curing, pathogenicity islands, DNA translocation, plasmid DNA degradation, cryo-EM structure
- MeSH terms
- Bacterial Proteins, DNA Helicases, DNA, Bacterial, Plasmids, Vibrio cholerae, Cryoelectron Microscopy, Genomic Islands, Protein Multimerization, Argonaute Proteins
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